Like Trigger said a million times, Ryuuko isn't the main character. Satuski is. Ryuuko is just a vehicle for the audience to experience the story of Satuski through.

Notice how she has been perfectly manipulated for the entire show and now they have perfectly aligning goals? Ryuuko doesn't have free thought, her every action is preplanned by Satsuki and she just does it. She's not a character so much as a plot device.